MICB425 Portfolio - Microbial Ecological Genomics: From Genomes to Biomes, Spring 2018

Module 01

Reserve the first level headings (#) for the start of a new Module. This will help to organize your portfolio in an intuitive fashion.
Note: Please edit this template to your heart’s content. This is meant to be the armature upon which you build your individual portfolio. You do not need to keep this instructive text in your final portfolio, although you do need to keep module and assignment names so we can identify what is what.

Module 01 portfolio check

The first of your second level headers (##) is to be used for the portfolio content checks. The Module 01 portfolio check has been built for you directly into this template, but will also be available as a stand-alone markdown document available on the MICB425 GitHub so that you know what is required in each module section in your portfolio. The completion status and comments will be filled in by the instructors during portfolio checks when your current portfolios are pulled from GitHub.

• Installation check
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• Portfolio repo setup
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• RMarkdown Pretty html Challenge
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• Evidence worksheet_01
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• Evidence worksheet_02
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• Evidence worksheet_03
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• Problem Set_01
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• Problem Set_02
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• Writing assessment_01
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• Additional Readings
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Data science Friday

The remaining second level headers (##) are for separating data science Friday, regular course, and project content. In this module, you will only need to include data science Friday and regular course content; projects will come later in the course.

Installation check

Third level headers (###) should be used for links to assignments, evidence worksheets, problem sets, and readings, as seen here.

Use this space to include your installation screenshots.

Portfolio repo setup

Detail the code you used to create, initialize, and push your portfolio repo to GitHub. This will be helpful as you will need to repeat many of these steps to update your porfolio throughout the course.

git add git commit -m“message” git push

and use git status to check

RMarkdown pretty html challenge

Paste your code from the in-class activity of recreating the example html.

version January 18, 2018

R Markdown PDF Challenge

The following assignment is an exercise for the reproduction of this .html document using the RStudio and RMarkdown tools we’ve shown you in class. Hopefully by the end of this, you won’t feel at all the way this poor PhD student does. We’re here to help, and when it comes to R, the internet is a really valuable resource. This open-source program has all kinds of tutorials online.

http://phdcomics.com/ Comic posted 1-17-2018

Challenge Goals

The goal of this R Markdown html challenge is to give you an opportunity to play with a bunch of different RMarkdown formatting. Consider it a chance to flex your RMarkdown muscles. Your goal is to write your own RMarkdown that rebuilds this html document as close to the original as possible. So, yes, this means you get to copy my irreverant tone exactly in your own Markdowns. It’s a little window into my psyche. Enjoy =)

hint: go to the PhD Comics website to see if you can find the image above If you can’t find that exact image, just find a comparable image from the PhD Comics website and include it in your markdown

Here’s a header!

Let’s be honest, this header is a little arbitrary. But show me that you can reproduce headers with different levels please. This is a level 3 header, for your reference (you can most easily tell this from the table of contents).

Another header, now with maths

Perhaps you’re already really confused by the whole markdown thing. Maybe you’re so confused that you’ve forgotton how to add. Never fear! A calculator R is here:

1231521+12341556280987

## [1] 1.234156e+13

Table Time

Or maybe, after you’ve added those numbers, you feel like it’s about time for a table! I’m going to leave all the guts of the coding here so you can see how libraries (R packages) are loaded into R (more on that later). It’s not terribly pretty, but it hints at how R works and how you will use it in the future. The summary function used below is a nice data exploration function that you may use in the ^future.

library(knitr)
kable(summary(cars),caption="I made this table with kable in the knitr package library")

I made this table with kable in the knitr package library

	speed	dist
	Min. : 4.0	Min. : 2.00
	1st Qu.:12.0	1st Qu.: 26.00
	Median :15.0	Median : 36.00
	Mean :15.4	Mean : 42.98
	3rd Qu.:19.0	3rd Qu.: 56.00
	Max. :25.0	Max. :120.00

And now you’ve almost finished your first RMarkdown! Feeling excited? We are! In fact, we’re so excited that maybe we need a big finale eh? Here’s ours! Include a fun gif of your choice!

)

Origins and Earth Systems

Evidence worksheet 01

The template for the first Evidence Worksheet has been included here. The first thing for any assignment should link(s) to any relevant literature (which should be included as full citations in a module references section below).

You can copy-paste in the answers you recorded when working through the evidence worksheet into this portfolio template.

As you include Evidence worksheets and Problem sets in the future, ensure that you delineate Questions/Learning Objectives/etc. by using headers that are 4th level and greater. This will still create header markings when you render (knit) the document, but will exclude these levels from the Table of Contents. That’s a good thing. You don’t’ want to clutter the Table of Contents too much.

Whitman et al 1998

Learning objectives

Describe the numerical abundance of microbial life in relation to ecology and biogeochemistry of Earth systems.

General questions

* What were the main questions being asked?

How do we estimate the prokaryotic population of the world? And what is it made up of?

What are the uncertainties that come with this measurement?

Which environments contain the most prokaryotic biomass?

How does this biomass affect global nutrient cycles? (e.g. P, C, N)

* What were the primary methodological approaches used?

Prokaryotic estimates were based upon average data from the following four environments: aquatic environments, soil, subsurface, and “other habitats” including in or on animal or plant surfaces or in the air. They used experimentally derived values to perform these calculations, but interestingly, not the same value sets for each environment. For example, some calculations included cell volume, while others included just the area of the environment. Vi

Also, they compared their calculated values with some from other papers, which resulted in some differences that they attempted to explain.

* Summarize the main results or findings.

They found that prokaryotes contain about half of the organic carbon on earth, and 90% of the nutrients (compared to plants) In brief, the prokaryotic biomass and thus their contribution to global cycles is very large - doubling estimates of the amount of carbon stored in living organisms globally. They broke down the calculations into four environments: aquatic environments, soil, subsurface, and “other habitats”.

Aquatic environments- this includes the open ocean, sediment in the ocean, freshwater and saline lakes (3 orders of magnitude less) and polar regions. Prokaryotes are ubiquitous in these environments - 1180 x 10²⁶ cells.

Soil- surprisingly, there are less prokaryotes in forest soils than in other soils. The estimates varied by ecosystem. 255.6 x 10²⁷ cells.

Subsurface- e.g. terrestrial habitats below 8 m and marine sediments below 10 cm. (this includes groundwater too) This environment is difficult to estimate because it is difficult to obtain uncontaminated samples. However, it has been suggested to be enormous. 3.8 x 10³⁰ cells.

Other environments - discussed the prokaryotes that live on animals, insects, and plants, and also those in the air/atmosphere. 53.024 x 10²³ cells (several orders of magnitude smaller)

These large numbers mean that not only carbon, but N and P are stored in globally significant amounts in prokaryotes.

Disproves Kluyver’s estimate that 1/2 of the living protoplasm on earth is microbial - likely this number is far too conservative. The paper also discusses growth rates to estimate cell turnover, and fluxes in and out of these environments.

* Do new questions arise from the results?

In subsurface environments, the turnover time of cells seems exceedingly large, is this a good estimate?

Where does the energy in the subsurface environments come from? Photosynthesis? Chemolithotrophy?

From the passage “in the polar regions, a relatively dense community of algae and prokaryotes forms at the water-ice interface” - why does this occur?

How accurate can these calculations be if they are based upon just a few estimates?

How much flux occurs among all of these prokaryotic environments? Especially the subsurface environment, if so many cells are hypothesized to be metabolically inactive, how much flux can occur? Is it more of a pool than a flux?

* Were there any specific challenges or advantages in understanding the paper (e.g. did the authors provide sufficient background information to understand experimental logic, were methods explained adequately, were any specific assumptions made, were conclusions justified based on the evidence, were the figures or tables useful and easy to understand)?

The estimates described in the paper introduce a large amount of uncertainty because no matter how many samples you collect, you are still having to generalize this data for the entire earth. You cannot possibly collect enough data to have any degree of accuracy in your prediction. However, otherwise, their experimental logic made sense.

Lastly, the estimates for each environment were likely collected using different methods- and by different people. Therefore, each method probably has its own pros and cons, and contributes its own level of uncertainty to the proceeding estimates.

Problem set 01

Whitman et al 1998 Kasting JF,and Siefert JL. 2003.

Learning objectives:

Describe the numerical abundance of microbial life in relation to the ecology and biogeochemistry of Earth systems.

Specific questions:

* What are the primary prokaryotic habitats on Earth and how do they vary with respect to their capacity to support life? Provide a breakdown of total cell abundance for each primary habitat from the tables provided in the text.

The primary prokaryotic habitats on earth are split into aquatic habitats, soil, and subsurface habitats. According to table 5 of the text, there are 12 x 10²⁸ cells in aquataic habitats, 26 x 10²⁸ cells in the soil, and interestingly, 355 x 10²⁸ and 25-250 x 10²⁸ prokaryotic cells in the oceanic and terrestrial subsurface respectively. However, in order to rank these habitats based on their capacity to support life, we must come up with a universal definition for “capacity to support life”. If you were to define this as the total number of prokaryotic cells in a given habitat, it would appear that the oceanic subsurface habitat has the greatest capacity to support life. However, this does not take into account whether these cells are metabolically active, or their turnover time, or the total area occupied by the habitat.

* What is the estimated prokaryotic cell abundance in the upper 200 m of the ocean and what fraction of this biomass is represented by marine cyanobacterium including Prochlorococcus? What is the significance of this ratio with respect to carbon cycling in the ocean and the atmospheric composition of the Earth?

2.8 x 10²⁸ cells in the upper 200m

The average density is 5 x 10⁵ cells/mL

To calculate what fraction of this ratio are cyanobacteria:

4 x10⁴ cells/ml / 5 x 10⁵ cells/ml x 100 = 8%

This ratio is significant because these cells are autotrophs, which means that they are responsible for asimilating inorganic carbon into this environment, and thus are an important aspect of carbon cycling in the ocean. This is not only important for aquatic environments, but for the atmospheric composition of the earth as well. This is because some organic carbon fixed by these autotrophs are not respired and stored in marine sediment. Since respiring this material generally requires oxygen, its long-tem storage means that oxygen can remain in significant levels in the earth’s atmosphere. This is in contrast to terrestrial systems, where carbon fixed by autotrophs is generally respired.

* What is the difference between an autotroph, heterotroph, and a lithotroph based on information provided in the text?

Autotroph - produces organic complex carbons from simple inorganic substances such as carbon dioxide. Heterotroph - takes up organic carbon to produce energy and synthesize compounds Lithotroph - uses an inorganic substrate to obtain reducing equivalents for use in biosynthesis or energy conservation via aerobic or anaerobic respiration

* Based on information provided in the text and your knowledge of geography what is the deepest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this depth?

Temperature is the limiting factor in subsurface environments, and at around 4 km in terestrial environments the temperature reaches 125 degrees celsius. This is the generally agreed upon temperature limit of prokaryotic life.

The deepest habitat capable of supporting prokaryotic life is the Mariana Trench, which is 10.9 km deep, then cellular life should be able to persist another 4 km deeper in the subsurface- so 14.9 km total.

* Based on information provided in the text your knowledge of geography what is the highest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this height?

Mount everest is 8.8 km high, so that would be the highest terestrial habitat capable of supporting prokaryotic life.

Additionally, in the text, bacteria in the air were discussed. However, are these bacteria actually metabolically active? They could just be spore formers, or metabolically inactive until they reach an environment that is more viable.

The paper stated 77 km, but this does not seem very realistic, because the limiting factors in these environments include nutrient availability, UV radiation, and temperature. So I would say more like 20 km high.

* Based on estimates of prokaryotic habitat limitation, what is the vertical distance of the Earth’s biosphere measured in km?

I would say that the vertical distance of the Earth’s biosphere is a range of 24 km - 34 km (due to the Mariana trench)

* How was annual cellular production of prokaryotes described in Table 7 column four determined? (Provide an example of the calculation)

Population size x turnovers/year = cells/year

Marine heterotrophs: 3.6 x 10²⁸ cells x 365 days / 16 days/turnover = 8.2 x 10²⁹ cells/year

* What is the relationship between carbon content, carbon assimilation efficiency and turnover rates in the upper 200m of the ocean? Why does this vary with depth in the ocean and between terrestrial and marine habitats?

Assuming the carbon efficiency is 20% If there is around 5-20 fg of carbon in a prokaryotic cell, 20 fg C/cell = 20^-30 Pg/cell

3.6 x 10²⁸ cells x 20^-30 Pg/cell = 0.72 Pg C are trapped in marine heterotrophs To calculate the total carbon flux, we should multiply this value by 5, but the authors used 4, so 4 x .72 = 2.88 Pg/year

51 Pg C/year, 85% of the carbon in the photic zone is consumed = 43 Pg C

43 Pg C/year / 2.88 Pg/year = 14.4 turnovers/year 1 turnover every 25.4 days

This varies with depth in the ocean due to access to sunlight, as photosynthesis provides the energy necessary for carbon fixation. In terestrial habitats, a number of factors including differences in depth, sediment, nutrient availability, and cell density contribute to the differences in carbon fixation and turnover rate.

* How were the frequency numbers for four simultaneous mutations in shared genes determined for marine heterotrophs and marine autotrophs given an average mutation rate of 4 x 10^-7 per DNA replication? (Provide an example of the calculation with units. Hint: cell and generation cancel out)

In table 7 of the paper, the turnover rate was discussed for each habitat, something that is essential for calculating the mutation frequency.

To calculate the frequency of four simultaneous mutations, (4x10^-7 per gene per DNA replication)⁴=2.56 x 10^-26 occurences per gene per DNA replication, in other words mutations per generation

Then we calculate the cell turnover, or the number of DNA replications that occur per hour for all the cells in the environment

3.6 x 10²⁸ cells x 22.8 turnovers/year = 8.2 x 10²⁹ cells/year 365 days / 16 days/turnover = 22.8 turnovers/year

Note: after this when I use the word mutation, this actually means the occurence of four simultaneous mutations

8.2 x 10²⁹ cells/year / 2.56 x 10^-26 mutations per generation = 2.1 x 10⁴ mutations/year

2.1 x 10⁴ mutations/year x 1 year/365 days = 57.53 mutations/day 57.53 mutations/day x 1 day/24 hours = 2.39 mutations/hour

In other words (the inverse of this ratio), 0.4 hours per four simultaneous mutation event.

* Given the large population size and high mutation rate of prokaryotic cells, what are the implications with respect to genetic diversity and adaptive potential? Are point mutations the only way in which microbial genomes diversify and adapt?

Given the large population size and high mutation rate of prokaryotic cells, this indicates that prokaryotic cells have a very large adaptive potential. As prokaryotes have existed on the earth for billions of years, this corresponds to an incredibly large amount of genetic diversity.

However, it is foolhardy to assume that point mutations are the only way that microbial genomes diversify and adapt. Infection by bacteriophages can transport foreign DNA into a cell, some cells can share plasmids using conjugative pili, and others can uptake exogenous DNA from their environment. Additionally, other mutation events can occur independent of point mutations in a single cell, such as gene duplication or deletion.

* What relationships can be inferred between prokaryotic abundance, diversity, and metabolic potential based on the information provided in the text?

Based on the information provided in the text, I would say that prokaryotic abundance and metabolic potential is highly related to the diversity of organisms present in the biosphere. Given the large abundance of prokaryotic life, and its correspondingly large mutation rate, over the course of geologic time this has generated an incredibly diverse set of metabolic capabilities of individual prokaryotes. These different metabolic abilities have enabled prokaryotes to colonize the entire biosphere (24-34 km of the earth’s surface, subsurface, and lower atmosphere).

Evidence Worksheet_02 “Life and the Evolution of Earth’s Atmosphere”

Learning objectives:

Comment on the emergence of microbial life and the evolution of Earth systems

• Indicate the key events in the evolution of Earth systems at each approximate moment in the time series. If times need to be adjusted or added to the timeline to fully account for the development of Earth systems, please do so.

  • 4.6 billion years ago

According to Nisbet et al, our solar system began after one or multiple supernova explosions. At this time, the inner planets (including earth) were formed from collisions between “planetesimals” - debris about the size of the earth’s moon.

+ 4.1 billion years ago  

The suggested origin of life (microbial) according to Nisbet et. al. Due to the intrinsically difficult nature of establishing an exact date, the origin of life is instead given in a range: 4.0+/-0.2 Gyr. This data is supported by specific carbon isotope signatures in zircons.

+ 3.8 billion years ago  

According to Nisbet et al, the earth suffered “frequent massive meteorite impacts”, some of which were large enough to cause the liquid water in the oceans to become steam.

This is when the earliest sedimentary rocks were found, which indicates that there were liquid oceans.

+ 3.5 billion years ago  

Fossil evidence of microbial biofilms and stromatolites first appears. Additionally, increased isotopic evidence for life. This is when Rubisco, the enzyme necessary for oxygenic photosynthesis was thought to have developed. This is when LUCA - the Last Universal Common Ancestor of all life was thought to have lived.

+ 3.0 billion years ago

First global glaciation event due to the presence of increasing amounts of oxygen in the earth’s atmosphere (oxygenic photosynthesis) which reacted with methane in the atmosphere. During this time the sun was much weaker, so the earth would have frozen earlier had it not been for methanogenesis contributing greenhouse gasses to keep the earth warm.

+ 2.7 billion years ago  

Increasing rise of atmospheric O₂, believed to be due to the rise of cyanobacteria. This is also when one of the first glaciation events occured, due to the decrease of CH₄ in the atmosphere due to microbial processes.

+ 2.2 billion years ago  

There are some findings that hypothetically date life on land beginning as early as 2.2 billion years ago. However, microbial fossils are far from conclusive.

+ 2.1 billion years ago

The advent of the first complex (read, multicellular) organisms, or at least fossil evidence for them.

+ 1.3 billion years ago

Evidence of the first land fungi and microbes: not photosynthetic land plants. Photosynthetic land plands were only thought to have evolved around 400 million years ago.

+ 550,000,000 years ago

The Cambrian explosion, when most modern day animal phyla are thought to have evolved. This was a major diversification of complex life on the planet.

+ 200,000 years ago

The first record of Homo Sapiens (us) in Africa.

• Describe the dominant physical and chemical characteristics of Earth systems at the following waypoints:

  • Hadean

The Hadean is generally established as 4.6 - 4 Gyr, and is contains the origin of earth as a planet to the origin of life on earth. During this time, meteorite bombardment levels were very high, and conditions on the surface were not well suited to life today. Initially, the earth was molten until after 4.5 billion years ago when the moon was formed. Nisbet et. al compares the Hadean earth to a “Norse Ice-Hades” with glacial temperatures interspersed with very high temperatures as a result of meteorite impacts. The oceans formed during this time period. Additionally, the early sun was fainter.

+ Archean  

Life developed during the Archaean (4-2.5 Gyr). Volcanic activity was very high, and due to the advent of oxygenic photosynthesis, the beginning of the oxygenation of the earth’s atmosphere occured.

+ Precambrian  

The Precambrian Supereon stretches from 4.6 Gyr - 0.56 Gyr, and contains the Hadean, Archean, and Proterozoic (but not the Phanerozoic) eons. The Earth went through a wide variety of physical and chemical characteristics during this time (see other sections for details).

+ Proterozoic  

2.5-0.56 Gyr. Oxygenation of the earth’s atmosphere continued, finally reaching significant levels due to the proliferation of oxygenic photosynthesis. This established conditions necesary for the first complex and multicellular organisms. As the sun’s luminosity increases by 6% every billion years, the earth begins to recieve more heat from the sun. However, there is evidence that the earth cooled during this period, a hypothesis known as Snowball Earth due to changes in the cheical composition of the atmosphere. There were likely repeated cycles of glaciation.

+ Phanerozoic  

0.56 Gyr to present day. This eon encompasses the development of land plants and land life, as well as the origins of most of the recognized animal phyla to this day. This comparatively small (considering the extent of the precambrian superepoch) epoch also contains several planetary extinction events establishment of land masses as we know them today.

Problem set 02

Learning objectives:

Discuss the role of microbial diversity and formation of coupled metabolism in driving global biogeochemical cycles.

Specific Questions:

* What are the primary geophysical and biogeochemical processes that create and sustain conditions for life on Earth? How do abiotic versus biotic processes vary with respect to matter and energy transformation and how are they interconnected?

According to Falkowski et al, the primary geophysical and biochemical processes that create and sustain conditions for life on Earth are plate tectonics and atmospherical photochemical processes. These phenomenon “supply substrates and remove products” necessary for avoiding planetary thermodynamic equilibrium at which point substrates essential for life on earth would be depleted. Abiotic and biotic processes are related in that together they establish the “average redox state” of the planet. The difference between abiotic and biotic processes is partially that of time scale, due to biological enzymes that can catalyze reactions, biotic processes can occur at greater speed, even if biotic and abiotic reactions are equally thermodynamically favorable. Additionally, biotic processes can drive oxidation based on photosynthesis, a unique energy transduction process.

* Why is Earth’s redox state considered an emergent property?

According to a reasearchgate post, “An emergent property is a property which a collection or complex system has, but which the individual members do not have.” Thus, since earth’s redox state is a product of biotic and abiotic processes, e.g. feedback between microbial metabolism and geochemical events - for context think about the “snowball earth” phenomenon after the advent of oxygenic photosynthesis, this is an emergent property. Individual populations of microbes do not establish the earth’s redox state, but collectively their interactions with geochemical processes do.

* How do reversible electron transfer reactions give rise to element and nutrient cycles at different ecological scales? What strategies do microbes use to overcome thermodynamic barriers to reversible electron flow?

To describe this process, I will use the example outlined in the Falkowski paper, that of the global nitrogen cycle, which before human intervention was run excusively by microbes. In this case, the different reversible (except for N₂ to NH₄ which only biologically occurs in one direction) reactions are mediated by different kinds of bacteria. These bacteria can be spatially separated, and use different forms of nitrogen as different kinds of substrates (as terminal electron acceptors, or as an electron donor in the case of nitrifying bacteria). The thermodynamic favorability of each reaction is also influenced by the availablility of other substrates (oxygen, organic matter) to help overcome thermodynamic barriers to reversible electron flow.

* Using information provided in the text, describe how the nitrogen cycle partitions between different redox “niches” and microbial groups. Is there a relationship between the nitrogen cycle and climate change?

The Falkowsi paper describes how the nitrogen cycle partitions between different redox niches and microbial groups. The paper states that “[t]ypically, reduction and oxidation reactions are segregated in different organisms”, and this is especially true in the nitrogen cycle. Some bacteria fix nitrogen, i.e. convert N₂ gas into NH₄. Other nitrifiers (archaea) oxidize ammonia to NO₂^-, and still others convert NO₂^- to NO₃^-. Finally, yet other bacteria reverse the cycle use NO₂^- and NO₃^- as terminal electron acceptors in the absence of nitrogen, thus re-forming N₂. The Canfield paper describes the relationship between the nitrogen cycle and climate change. Specifically, N₂O, a part of the nitrogen cycle, is a potent greenhouse gas.

* What is the relationship between microbial diversity and metabolic diversity and how does this relate to the discovery of new protein families from microbial community genomes?

Metabolic diversity is not as large as, say, diversity in “boutique” or nonessential genes specific to particular environments. This is because metabolic genes are essential, and make up components of “multimeric microbial machines”. Thus, they are more evolutionarily constrained than other kinds of genes due to their required interaction with other genes in the essential processes of energy transduction, DNA replication, et. cetera. Thus, even genes encoding imperfect proteins and enzymes (the Falkowski paper uses the D1 protein of photosystem II as an example) remain evolutionarily conserved. However, as other “nonessential” genes are not constrained in this manner, the discovery of new protein families is directly correlated with the sheer volume of sampling performed. It is these genes that show the extent of the microbial diverersity that has evolved over the last 4 billion years or so.

* On what basis do the authors consider microbes the guardians of metabolism?

Microbes are guardians of metabolism in that they preserve the metabolic pathways essential for life on earth, even if individual bacteria do not perform this specific reaction themselves. This allows a metabolic pathway to survive even when some of the bacteria that perform it become extinct. This is partially due to the phenomenon of horizontal gene transfer. Additionally, they control the ways that electrons flow on the planet’s surface (and to some extent subsurface), and over billions of years have contributed to the formation of the current redox state of the earth as a whole.

Evidence worksheet 03

I choose the paper “A safe operating space for humanity” by Rockstrom et al

* What were the main questions being asked?

What are the “planetary boundaries” that define environmental change in the Anthropocene? How do we identify and quantify these boundaries? How much “wiggle room” does humanity have to surpass these boundaries? How do these biogeochemical processes which mark the planetary boundaries effect one another?

* What were the primary methodological approaches used?

This particular paper was really more of a review, or a compilation of previously published or estimated data incorporated into a new context. Therefore, there wasn’t really a methods section. They were very careful to explain the limitations of drawing larger conclusions from these larger scale data sets, and the limitations in collecting data concerning specific planetary boundaries. For example, in table 1, atmospheric aerosol loading and chemical polution both had no data sets to display.

* Summarize the main results or findings.

They identified nine planetary boundaries: “climate change; rate of biodiversity loss (terrestrial and marine); interference with the nitrogen and phosphorus cycles; stratospheric ozone depletion; ocean acidification; global fresh- water use; change in land use; chemical pollution; and atmospheric aerosol loading” The paper presents evidence that three of these boundaries have been overstepped.

* Do new questions arise from the results?

To what degree do environmental perturbations affect each other? The paper mentions “long term reinforcing feedback processes” such as decreases in vegetation cover that contribute to further climate change. The paper states that “If one boundary is transgressed, then other boundaries are also under serious risk.”" How would one quantify chemical pollution and atmospheric aerosol loading in a global setting? What is the timeline for the effects of transgressing environmental boundaries to become visible? Does it depend on the specific boundary that was crossed?

* Were there any specific challenges or advantages in understanding the paper (e.g. did the authors provide sufficient background information to understand experimental logic, were methods explained adequately, were any specific assumptions made, were conclusions justified based on the evidence, were the figures or tables useful and easy to understand)?

The paer mentions staying on the “safe side” of atmospheric and enviromental boundaries, but it doesn’t mention where exactly this is. To be fair, this a very difficult thing to quantify or even estimate. It also depends on your definition of “safe”

Writing Assignment

Victoria Panwala

Student Number: 14028147

Module 1 Writing Assignment

Prompt: “Microbial life can easily live without us; we, however, cannot survive without the global catalysis and environmental transformations it provides.” Do you agree or disagree with this statement? Answer the question using specific reference to your reading, discussions and content from evidence worksheets and problem sets.

Microbial life exists all around us. Microbes persist up to 4 kilometers below our feet, and 20 kilometers above our heads(1). Indeed, it is difficult to find an environment on earth that has not been colonized in some way by microbial life. Thermophilic bacteria can survive in temperatures up to 122 C(2), and chemoautotrophs have even evolved to obtain energy from the oxidation of substances like hydrogen sulfide(3). Not only have microbes been involved in making the earth habitable for multicellular life, they are also responsible for creating the environmental conditions essential for life today. Processes such as the nitrogen cycle, the carbon cycle, the production of vitamins, and the decomposition of recalcitrant materials could not proceed at the same rates without input from microbes. Thus, if not for microbial life, humans would not, and could not, exist.

While the exact time frame of life’s appearance on our planet is hotly debated – geological evidence points to somewhere between 4 and 3.5 billion years ago – its microbial nature is not(4). Microbes existed for billions of years before complex multicellular life arose, and transformed the environment of the early earth. Before the advent of oxygenic photosynthesis carried out by cyanobacteria, the Archaean Earth was an anoxic place. Methanogens, likely archaea, created an atmosphere which contained much more methane than the one that exists today. The greenhouse effects of this methane exerted a warming effect on the early earth, compensating for a sun that was considerably dimmer(5). Once oxygenic photosynthesis became a prominent contributor to the oxygen content of the earth’s atmosphere, this altered environmental conditions considerably. For example, this phenomenon allowed for the formation of the ozone layer that we rely on for protection today(5). In fact, even now that multicellular eukaryotic plants are also capable of performing photosynthesis, heterotrophic respiration requiring oxygen negates most of the oxygenic input from terrestrial systems. It is only in marine environments, where photosynthesis is performed primarily by microbes, that a net source of oxygen is released to the earth’s atmosphere. This is because a small amount of organic matter synthesized by these microbes is “buried” in marine sediments, away from oxygen consuming heterotrophs(5). Thus, microbes in general, and oxygenic cyanobacteria in particular, are responsible for creating the conditions required for life as we know it.

Although nitrogen gas makes up about 78% of our atmosphere, biologically available nitrogen sources are in somewhat shorter supply. In order to be utilized by organisms (including humans), nitrogen gas must first be fixed from its inert N2 gas form. The processes of nitrification and denitrification- which closes the nitrogen cycle by once again creating inert N2 gas- are both catalyzed by microbes(6). Indeed, eukarya do not possess the nitrogenase gene required for nitrogen fixation, it is only present in the microbial domains of archaea and bacteria(7). Even in the well-studied cases of nitrogen fixing bacterial symbionts living in the root nodules of legumes, horizontal gene transfer has not distributed this particular metabolic pathway between the two organisms(7). Forced to obtain ever greater amounts of nitrogen for food-production purposes, humankind has resorted to the industrial Haber Bosch process to produce ammonia-containing fertilizer. Nowadays, fossil fuel use and the Haber Bosch process account for 45% of the annual nitrogen fixation on earth(6). This is not an insignificant nitrogen fixation flux, but it is still folly to assume that humans could control the global nitrogen cycle without input from microbial sources. Aquatic environments still rely on microbial nitrogen-fixers to provide usable forms of nitrogen for primary production. Due to the importance of this environment as a carbon sink(8), the disappearance of this microbial pathway would have a large effect on oceanic production, and the global carbon cycle. Therefore, even though we are capable of fixing our own nitrogen, the regulation of the nitrogen cycle by prokaryotes is essential for our survival as a species.

The carbon cycle is yet another process that is fundamentally controlled by microbial processes. Microbial primary producers (such as cyanobacteria) and heterotrophic microbes serve as sinks for atmospheric CO2 and the sources of CO2 fluxes into the environment respectively(11). Even though increased anthropogenic CO2 fluxes from fossil fuels are becoming ever more of a concern, microbes in the soil contribute 10 times more of a CO2 flux globally(11). This decomposition and respiration of organic matter allows for the transformation of this organic material into forms that are once-again usable by other life-forms. This is especially true for complex organic polymers such as lignin, hemicellulose, and cellulose. Microbes produce and secrete extracellular enzymes that break down these complex structures so their components may be metabolized(11). Without this activity, it is undoubtable that organic material would not turnover at the rate that we are accustomed to today. This would have an enormous impact on essential human processes such as crop production.

Humans and other organisms require a variety of essential micronutrients to perform basic metabolic processes. Often, these micronutrients, also known as vitamins, are precursors or cofactors of metabolic enzymes. While many microbes can synthesize these on their own, humans must obtain most vitamins exogenously(9,10). Some of these vitamins are obtained from the food that we eat, and absorbed by the human digestive tract. Still others are synthesized by our very own microbiota that persists in the gastrointestinal tract. Metagenomic studies of human gut commensals have shown that collectively, they possess many of the biosynthetic pathways required for vitamin synthesis. B vitamins in particular (folate, riboflavin, B12, niacin, pyridoxine, et cetera) are often synthesized by lactobacilli living in the human gut(10). In a world without microbes, these essential biosynthetic processes would be halted, and humans and other organisms would become rapidly vitamin-deficient.

The truth of the matter is that we humans cannot survive without the global biogeochemical processes performed by microbes. Although individually tiny, their contributions on a global scale shape the world around us today. However, the question remains, how long can this global microbial metabolism continue to sustain us as a species? Human input into biogeochemical cycles has fundamentally altered the nitrogen and carbon cycles of our planet. How much longer can microbes continue to maintain earth’s systems as we know them today? Thanks to their rapid evolutionary capacity and astounding metabolic and environmental diversity, microbes will certainly survive all but the most catastrophic of environmental alterations. But due to our much more stringent environmental requirements for survival, humanity will not.

References:

1. Whitman WB, Coleman DC, and Wiebe WJ. 1998. Prokaryotes: The unseen majority. Proc Natl Acad Sci USA. 95(12):6578-6583. PMC33863

2. Takai T; et al. (2008). “Cell proliferation at 122°C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation” (PDF). PNAS. 105 (31): 10949-51. Bibcode:2008PNAS..10510949T. doi:10.1073/pnas.0712334105. PMC 2490668 

3. Nakagawa S, Takai K. 2008. Deep-sea vent chemoautotrophs: diversity, biochemistry, and ecological significance. FEMS Microbiology. Jul;65(1):1-14. doi: 10.1111/j.1574-6941.2008.00502 PMID:18503548

4. Nisbet EG, and Sleep NH. 2001. The habitat and nature of early life. Nature. 409: 1083-1091.

5. Kasting JF,and Siefert JL. 2003. Life and the Evolution of Earth’s Atmosphere. Science. 296: 1066-1067. (https://www.ncbi.nlm.nih.gov/pubmed?term=Science%5BJour%5D+AND+Life+and+the+Evolution+of+Earth's+Atmosphere&TransSchema=title&cmd=detailssearch)

6. Canfield DE, et al. 2010. The Evolution and Future of Earth’s Nitrogen Cycle. Science 330, 192 (2010);DOI: 10.1126/science.1186120

7. Soto G1, Fox AR, Ayub ND. 2013. Exploring the intrinsic limits of nitrogenase transfer from bacteria to eukaryotes. Journal of Molecular Evolution. Aug;77(1-2):3-7. doi: 10.1007/s00239-013-9578-8. Epub 2013 Aug 11. PMID:23933654

8. Falkowski P, et al. 2000. “The Global Carbon Cycle: A test of our knowledge of earth as a system. Science’s Compass: Review. April 3, 2013.

9. Burkholder, P. R., & McVeigh, I. (1942). Synthesis of Vitamins by Intestinal Bacteria. Proceedings of the National Academy of Sciences of the United States of America, 28(7), 285-289.

10. LeBlanc, J. G., Milani, C., de Giori, G. S., Sesma, F., van Sinderen, D., & Ventura, M. (2013). Bacteria as vitamin suppliers to their host: A gut microbiota perspective. Current Opinion in Biotechnology, 24(2), 160-168. 10.1016/j.copbio.2012.08.005

11. Gougoulias, C., Clark, J. M., & Shaw, L. J. (2014). The role of soil microbes in the global carbon cycle: tracking the below-ground microbial processing of plant-derived carbon for manipulating carbon dynamics in agricultural systems. Journal of the Science of Food and Agriculture, 94(12), 2362-2371. http://doi.org/10.1002/jsfa.6577

Module 01 references

Utilize this space to include a bibliography of any literature you want associated with this module. We recommend keeping this as the final header under each module.

An example for Whitman and Wiebe (1998) has been included below.

Whitman WB, Coleman DC, and Wiebe WJ. 1998. Prokaryotes: The unseen majority. Proc Natl Acad Sci USA. 95(12):6578–6583. PMC33863

Kasting JF,and Siefert JL. 2003. Life and the Evolution of Earth’s Atmosphere. Science. 296: 1066-1067. (https://www.ncbi.nlm.nih.gov/pubmed?term=Science%5BJour%5D+AND+Life+and+the+Evolution+of+Earth’s+Atmosphere&TransSchema=title&cmd=detailssearch)

Nisbet EG, and Sleep NH. 2001. The habitat and nature of early life. Nature. 409: 1083-1091.

Orndoroff RC, et al. 2007. Divisions of Geologic Time - Major Chronostratigraphic and Geochronologic Units. Fact Sheet 2007-3015. U.S. Department of the Interior and U.S. Geological Survey.

Falkowski PC, et al. 2008. The Microbial Engines That Drive Earth’s Biogeochemical Cycles. Science 320, 1034 (2008);DOI: 10.1126/science.1153213

Canfield DE, et al. 2010. The Evolution and Future of Earth’s Nitrogen Cycle. Science 330, 192 (2010);DOI: 10.1126/science.1186120

Rockstrom J, et al. 2009. “A safe operating space for humanity” Nature.